Microbiological Identification Research Articles

Histologic Features of Mycobacterial Spindle Cell Pseudotumors: A Multi-institutional Clinicopathologic Analysis of 14 Cases.

Mycobacterial spindle cell pseudotumors (MSPs) are a rare and diagnostically challenging manifestation of non-tuberculous mycobacterial (NTM) infections. Proper recognition of these pseudotumors is important because they are treatable and benign. In this study, we evaluated the morphologic patterns of MSPs to improve their pathologic identification. Clinical and morphologic features of 14 MSPs were analyzed. Histologic factors evaluated included the architectural growth pattern of spindled or epithelioid macrophages, granulomas and their location within the lesion, neutrophilic microabscesses, multinucleated giant cells, necrosis, and effacement of background tissue. The composition of inflammatory infiltrates, organism density by acid-fast staining, and stromal changes were also assessed. In addition, 8 of 14 cases underwent molecular microbiology identification by a clinical amplicon-sequencing assay for non-tuberculous mycobacteria. MSP sites included 2 bowel, 10 lymph nodes, 1 liver, and 1 extremity. Cases with available clinical history (n=10) all occurred in immunocompromised patients. All demonstrated effacement of normal structures with spindled cells arranged in a storiform or fascicular architectural pattern. In addition, all cases showed lymphocytic inflammation, with prominent concurrent neutrophilic inflammation in 50% (7/14) of cases. Other morphologic findings included foamy histiocytes (64%, 9/14), peripherally situated granulomas (21%, 3/14), and neutrophilic microabscesses (21%, 3/14). All tested cases were positive for NTM by PCR methods. Mycobacterium avium was the most commonly isolated pathogen (6/8). Mycobacterial spindle cell pseudotumors show predominantly spindled morphology that may be mistaken as a neoplasm. Surgical pathologists who evaluate lymph nodes, soft tissue, and gastrointestinal tissues should be aware of this spindled tumefactive phenomenon in the setting of immunocompromised patients. Recognition of key morphologic features of neutrophilic inflammation, peripheral granulomas, or foamy histiocytes within a spindled lesion can help guide the pathologist to a correct diagnosis of an inflammatory process secondary to infection rather than a spindle cell neoplasm. Accurate diagnosis to facilitate appropriate antimicrobial and/or surgical therapy requires a comprehensive evaluation combining clinical, histopathologic, and microbiological findings.

An observational study of farmer-reported clinical mastitis in New Zealand dairy ewes

ABSTRACT Aims To describe the incidence, aetiology, treatment, and outcomes of farmer-reported clinical mastitis on New Zealand dairy sheep farms. Methods A prospective cohort study was conducted on 20 spring-lambing New Zealand sheep milking farms over the 2022–2023 season. Clinical mastitis was defined as a change in the appearance of milk and/or signs of inflammation in the gland. Farmers were required to report all cases of clinical mastitis and collect information on affected ewes’ demographics, clinical features, treatments (where applicable), and outcomes. Milk samples from mastitic glands were submitted for microbiological culture and identification by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF). Results Partial or complete clinical mastitis data were available for 236 cases from 221 ewes on 18/20 study farms. Clinical mastitis was diagnosed in 0–6% of ewes at the farm level, with an overall incidence of 1.8 (95% CI = 1.0–3.2)% using the study data, or 2.3 (95% CI = 1.6–3.3)% using the study data and farmer estimates that included unreported cases. Cases occurred mostly in early lactation, with 59% detected during the lambing period (August–October), at a median of 7 (IQR 3, 40) days in milk. The majority of cases featured clots in the milk (59%), swelling (55%), and unevenness (71%) of the glands. Pyrexia (rectal temperature ≥ 40.0°C) was diagnosed in 25% of cases and depression (lethargy, inappetence, or inability to stand) in 26% of cases. Treatment was given to 46% of cases, with tylosin being the most commonly used treatment (50% of treated cases). The most common outcome was immediate drying off to be culled without treatment (32%), followed by still milking and recovered but with lasting problems (25%). Nearly half of all the milk samples submitted were culture negative. Streptococcus uberis (14%), non-aureus staphylococci (12%), and Staphylococcus aureus (11%) were the most common isolates, found on 12, 8 and 8 of the 16 farms with microbiological data, respectively. Conclusions Clinical mastitis affected up to 6% of ewes at the farm level. Systemic signs were observed in one quarter of affected ewes, suggesting a role for supportive treatment. Clinical mastitis can be severe and challenging to fully resolve in New Zealand dairy sheep. Clinical relevance This is the first systematic study of clinical mastitis in New Zealand dairy ewes. It provides baseline information specific to New Zealand conditions for farmers, veterinarians, and other advisors to guide the management of mastitis for the relatively new dairy sheep industry in New Zealand.

Utility of a multiplex pathogen detection system directly from respiratory specimens for treatment and diagnostic stewardship.

The availability of syndrome-based panels for various ailments has widened the scope of diagnostics in many clinical settings. These panels can detect a multitude of pathogens responsible for a particular condition, which can lead to a timely diagnosis and better treatment outcomes. In contrast to traditional identification methods based on pathogen growth on culture, syndrome-based panels offer a quicker diagnosis, which can be especially beneficial in situations requiring urgent care, such as intensive care units. One such panel is the Biofire Filmarray Pneumonia plus Panel (BFP), which we have compared against microbiological culture and identification. The lower respiratory samples from patients were tested with BFP, culture, and identification with culture considered the gold standard. The phenotypic antibiotic susceptibility results (Vitek 2) were compared with the antimicrobial resistance (AMR) genes detected in BFP. Statistical analysis was carried out using GraphPad 7.0 and MS Excel (Microsoft Inc.). The results showed a positive percent agreement of 100% and a negative percent agreement of 47.8% with an overall agreement of 76.72% compared to culture. BFP was better at identifying fastidious bacteria, and the agreement with culture was higher for high bacterial identification numbers (107 and 106). There was also a correlation between the number of pathogens detected and growth in culture. Carbapenemase genes were detected in around 80% of phenotypically resistant samples and correlated with in-house PCR 60% of the time. Hence, BFP results need to be interpreted with caution especially when multiple pathogens are detected. Similarly, the presence or absence of AMR genes should be used to guide the therapy while being watchful of unusual resistance or susceptibility. The cost constraints and low throughput call for patient selection criteria and prioritization in emergency or resource-limited conditions.IMPORTANCEApplication of syndrome-based panels in clinical microbiology is of huge support in infectious conditions requiring urgent interventions, such as pneumonia. Interpreting the results requires caution; hence, we have compared the results obtained from Biofire Filmarray Pneumonia plus Panel with standard microbiological methods.

Microbiological identification of some culturable native strains associated with the digestive tract in Panaque cochliodon

Objective. To characterize by microbiology the native strains associated to the intestinal tract of the species Panaque cochliodon. Materials and methods. Three adult specimens captured in the Magdalena River that were transported and sacrificed under animal welfare regulations were used. Dissection of the intestinal tract was performed, obtaining samples for microbiological isolation, using culture media, purifying the microorganisms, performing metabolic biochemical tests and API 20E (Biomeriux) tests for their identification. Results. Information on the microbial population structure was obtained, reporting the phylum Proteobacteria with the species: Pantoea sp, Erwinia sp, Providencia stuarti, Providencia alcalifaciens, Serratia ficaria, Citrobacter koseri and the phylum Firmicutes with the species: Bacillus sphaericus, Bacillus subtilis, Bacillus thurigiensis, Bacillus mycoides, Bacillus coagulans and Bacillus circulans. Conclusion. The predominant culturable microorganisms in P. cohliodon belong to the phylum Proteobacteria and the phylum Firmicutes.

Microbial keratitis and its management at a rural centre: achieving success with limited resources.

Microbial keratitis is a sight-threatening condition with a higher incidence in agrarian populations. In countries with a high indigent population, due to financial and other constraints, patients prefer to seek therapy locally rather than travel to advanced centres. The aim of this study is to describe the epidemiology, clinical characteristics, and outcomes of 60 consecutive patients with microbial keratitis managed at a rural centre. Descriptive case series. All patients clinically diagnosed with infectious keratitis were included. Corneal scrapings were obtained and microbiological identification was done by Gram stain. Anti-microbial therapy was commenced based on smear findings and the patients were followed up till disease resolution. Sixty eyes of 60 patients were diagnosed with microbial keratitis in the study period. The mean age was 47.43 ± 18.69years. Male:female ratio was 47:53. Risk factors included ocular trauma in the majority of patients (46/60; 76.7%). Microorganisms were identified on 75.6% of smears, with fungal filaments (65.4%) being the most common. Ulcers were central in over half (32/60; 53.3%), and > 3mm in diameter in over three-fourths (81.6%) of patients. Forty-four patients (73.3%) achieved treatment success whereas 16/60 (26.6%) required referral to our tertiary-eye care facility for management. The median time to resolution was 14days (IQR 10-26days). Our series demonstrates the feasibility of microbiology-guided therapy in microbial keratitis by ophthalmologists at the secondary rural eye-care level. Two-thirds of the patients could be successfully managed at the rural centre and only severe cases needed a referral to tertiary centres.

Clinical, phenotypic, and genotypic characteristics of ESBL-producing Salmonella enterica bloodstream infections from Qatar

BackgroundResistant Salmonella infections are a major global public health challenge particularly for multidrug-resistant (MDR) isolates manifesting as bloodstream infections (BSIs). ObjectivesTo evaluate clinical, phenotypic, and genotypic characteristics of extended-spectrum beta-lactamase (ESBL) producing Salmonella enterica BSIs from Qatar. MethodsPhenotypic ESBL Salmonella enterica from adult patients presenting with positive BSIs were collected between January 2019 to May 2020. Microbiological identification and characterization were performed using standard methods while genetic characteristics were examined through whole genome sequencing studies. ResultsOf 151 episodes of Salmonella enterica BSI, 15 (10%) phenotypic ESBL isolates were collected. Recent travel was recorded in most cases (80%) with recent exposure to antimicrobials (27%). High-level resistance to quinolines, aminoglycosides, and cephalosporins was recorded (80-100%) while meropenem, tigecycline and colistin demonstrated universal susceptibility. Genomic evaluation demonstrated dominance of serotype Salmonella Typhi sequence type 1 (93%) while antimicrobial resistance genes revealed dominance of aminoglycoside resistance (100%), qnrS1 quinolones resistance (80%), blaCTX-M-15 ESBLs (86.7%), and paucity of AmpC resistance genes (6.7%). ConclusionsInvasive MDR Salmonella enterica is mainly imported, connected to patients from high prevalent regions with recent travel and antimicrobial use caused by specific resistant clones. In suspected cases of multidrug resistance, carbapenem therapy is recommended.

Aerobic Microbiological Spectrum and Antibiotic Resistance in Children Operated for Anorectal Abscesses.

(1) Background: Anorectal abscesses are a relatively rare pathology in childhood. Most often, male children under 1 year of age are affected. The importance of microbiological examination for the diagnosis and treatment of such patients remains debatable among surgeons, resulting in scarce data being available in the literature. We aimed to identify the aerobic microbiological spectrum and antibiotic resistance of isolates in children undergoing operation to treat anorectal abscesses. (2) Methods: We performed a case series of 102 children diagnosed and operated for anorectal abscesses over a period of 10 years (2010-2019). Purulent wound exudate was used for microbiological evaluation, which was subsequently cultured on 5% sheep-blood agar and eosin-methylene blue agar. For microbiological identification, conventional biochemical tests and semi-automated (API 20, bioMerieux, Marcy-l'Étoile, France) tests were used, as well as automated systems (Vitek-2 Compact, bioMerieux, France). Antimicrobial susceptibility testing was performed by the disk diffusion method of Bauer-Kirby and by determining the minimal inhibitory concentrations for glycopeptides. The results were interpreted according to the EUCAST standard for the corresponding year. (3) Results: Microbiological testing in children operated for anorectal abscesses mainly identified the gut commensals that normally reside in the rectal mucosa. Monocultures were found in just over half of the cases. Escherichia coli, Klebsiella pneumoniae complex, and Proteus mirabilis were the most frequently isolated. In addition, Staphylococcus aureus was found in 7% of patients. In Gram-negative bacteria, antibiotic resistance was most often observed in penicillins, cephalosporins, sulfonamides, and fluoroquinolones. (4) Conclusions: The increasing rates of antimicrobial resistance impose the need for the local monitoring of circulating commensal bacteria associated with anorectal abscesses in children to guide antibiotic therapy when indicated.

Combined Mutual Learning Net for Raman Spectral Microbial Strain Identification.

Infectious diseases pose a significant threat to global health, yet traditional microbiological identification methods suffer from drawbacks, such as high costs and long processing times. Raman spectroscopy, a label-free and noninvasive technique, provides rich chemical information and has tremendous potential in fast microbial diagnoses. Here, we propose a novel Combined Mutual Learning Net that precisely identifies microbial subspecies. It demonstrated an average identification accuracy of 87.96% in an open-access data set with thirty microbial strains, representing a 5.76% improvement. 50% of the microbial subspecies accuracies were elevated by 1% to 46%, especially for E. coli 2 improved from 31% to 77%. Furthermore, it achieved a remarkable subspecies accuracy of 92.4% in the custom-built fiber-optical tweezers Raman spectroscopy system, which collects Raman spectra at a single-cell level. This advancement demonstrates the effectiveness of this method in microbial subspecies identification, offering a promising solution for microbiology diagnosis.

The clinical, microbiological, and demographic aspects of Burkholderia infections: insights from a tertiary healthcare setting

Background and objectives. Optimal management requires an understanding of Burkholderia infections demographic, clinical, microbiological, and antibiotic features. This study aims to improve treatment and infection control strategies by investigating the clinical profiles and antibiotic susceptibilities of Burkholderia infections in a tertiary care context. Material and Methods. A retrospective analysis of 48 individuals with Burkholderia infections was carried out in a tertiary care environment. We gathered and analyzed data on antimicrobial susceptibility, clinical presentation, microbiological identification, and demographic features. Results. The mean age of the participants was 49.27 years, and their gender distribution was equal. Diabetes, heart disease, and hypertension are common comorbidities. The most typical symptoms were fever and cough, with infections varying in severity from minor to severe. Burkholderia was predominantly found in urine, blood, and respiratory secretions. Testing for antibiotic susceptibility showed inconsistent findings; some drugs, including ceftazidime and meropenem, were more successful than others. Conclusion. The research highlights the broad demographics impact of Burkholderia infections, in addition to their acute and occasionally fatal characteristics. It highlights how important it is to treat every patient differently, accounting for comorbidities and the severity of symptoms. The results emphasize how much more study is required to improve treatment options and learn more about the origins of Burkholderia infections.

Investigation of the Multidrug Resistance Pattern of Bacteria Isolated from Car and Office Door Handles in a Tertiary Institution

Multidrug-resistant bacteria have posed a public health concern over the years, especially with the difficulty and cost of treatment of infections they cause. Fomites such as door handles are thus potent means through which pathogens are transmitted from one person to another as contact with them is made. This study thus involves isolating antibiotic-resistant bacteria from car and office door handles in a university environment. Using the simple random sampling method, twenty samples (20) from car door handles and twenty samples (20) from office door handles were collected, the isolation of bacteria was done using standard microbiological procedures and identification of the isolates was done using cultural, microscopic and biochemical characterization. Determination of the antibiotic sensitivity pattern of the isolates was done using the Kirby-Bauer disc diffusion method on Muller Hinton agar. Antibiotics used included Ofloxacin (5 µg), Gentamicin (10 µg), Ceftriaxone (30 µg), Augmentin (30 µg), Ciprofloxacin (5 µg), Erythromycin (5 µg), Streptomycin (30 µg) and Cloxacillin (30 µg). The results showed a significant frequency of occurrence of Staphylococcus aureus at 35% and Klebsiella pneumoniae having least at 5%. From car door handles, S. epidermidis recorded 37% while K. pneumoniae recorded the least with 17.4%. The isolates exhibited resistance to antibiotics including Augmentin and Ceftriaxone (≤22 mm) while they were more susceptible to Ofloxacin (≥16 mm). All the K. pneumoniae isolated from car door handles exhibited resistance to Augmentin and Ceftriaxone. These results show that these surfaces could be a possible reservoir of infections caused by resistant bacteria, leading to difficulty in the treatment of infections caused by them.

Isolation and Identification of Biofilm forming Bacteria from Glass Panels exposed in Sea Waters of South Andaman, India

Marine organisms attach to surfaces that are submerged in seawater in a process known as biofouling. These organisms can colonize on various surfaces such as ship hulls, pillars, jetties, undersea pipelines, oil rigs and buoys. Foulers can include bacteria, algae, barnacles, mussels and other invertebrates. The initial adhesion of fouling bacteria is the first stage of biofouling. The growth and attachment of marine fouling bacteria are influenced by various environmental factors including salinity, temperature and nutrient availability. The bacteria forming marine biofilm were isolated and identified from glass panels. Basic microbiological phenotypic identification methods and genotypic validation using 16s rRNA gene sequencing were used to identify the bacterial strains. The phylogenetic analysis of the 16s rRNA gene sequences confirmed 13 different species (Bacillus aquimaris (2), Vibrio hepatarius (1), Exiguobacterium profundum (3), Exiguobacterium aestuarii (2), Vibrio parahaemolyticus (2), Vibrio alginolyticus (3), Vibrio azureus (2), Vibrio fluvialis (2), Priestia flexa (1), Pseudomonas aeruginosa (2), Bacillus megaterium (2), Lysinibacillus macroides (2) and Bacillus subtilis (1)) of fouling bacteria belonging to six genera.

Prevalence of extended-spectrum beta-lactamase and molecular detection of blaTEM, blaSHV, and blaCTX-M genotypes among gram-negative Bacilli isolates from hospital acquired infections in pediatrics, one institutional study

BackgroundGram-negative bacilli represents an important pathogen in hospital-acquired infections (HAIs) worldwide. The emergence of antibiotic resistance in these pathogens warrants attention for the proper management of infections. Extended-spectrum beta-lactamase (ESBL) resistance represents a major therapeutic problem in infections due to Gram-negative bacilli.The present study aimed to study the extended-spectrum beta-lactamase genes blaTEM, blaSHV, and blaCTX-M by multiplex polymerase reaction in isolated Gram-negative bacilli from HAIs in pediatric patients.MethodsThe study included one hundred-five isolates of Gram-negative bacilli from pediatric patients with different types of HAIs. The isolates were subjected to full microbiological identification, antibiotics susceptibility by disc diffusion method, the phenotypic study of ESBL, and the genetic study of ESBL genes by multiplex PCR.ResultsFifty isolates of Gram-Negative bacilli showed ESBL activity by a phenotypic study by double disc diffusion method (50/105). All ESBL producers’ isolates were positive by PCR for ESBL genes. The most frequent gene was blaTEM (64%), followed by blaSHV (30%) and CTX-M (22%). Mixed genes were found in 4 isolates (8%) for blaTEM and blaSHV, blaTEM and CTX-M. There was a significant association between PCR for ESBL genes and phenotypic ESBL detection (P = 0.001). There was significant detection of ESBL genes in E. coli (28%), followed by Enterobacter spp. (26%), Klebsiella spp. (24%), Serratia (14%), Pseudomonas spp. (6%) and Proteus (2%), P = 0.01. There Seventy percent of isolates positive for ESBL production had an insignificant association between MDR and PCR for ESBL genes (P = 0.23).ConclusionThe present study highlights the prevalence of ESBL activity among clinical isolates of Gram-negative bacilli isolated from hospital-acquired infections in pediatric patients. The most common gene responsible for this activity was blaTEM gee followed by blaSHV and blaCTX-M. There was a high prevalence of multiple antibiotic resistance among isolates with ESBL activity. The finding of the present study denotes the importance of screening extended beta-lactamase among Gram-negative bacilli associated with HAIs in pediatric patients.

VATS-visualisatie van een ernstige pulmonale infectie met Nocardia nova resistent tegen trimethoprim-sulfamethoxazol

Severe pulmonary Nocardia nova infection in a kidney transplant patient This article describes the disease course of a severe Nocardia nova infection in a patient with an underlying immunodeficiency due to a kidney transplantation, with the visualisation of Nocardia colonies in the pleural cavity through video-assisted thoracoscopic surgery. The patient was hospitalised in the emergency department with acute respiratory symptoms and respiratory failure. A CT scan of the chest revealed a massive unilateral pleural effusion with complete compressive atelectasis of the left lung. Video-assisted thoracoscopic surgery revealed bloody pleural effusion and white, nodular, pleural structures. Cultures of the biopsies grew N. nova. The empiric antibiotic treatment was switched to a combination therapy with trimethoprim-sulfamethoxazole, meropenem and a single dose of amikacin. Sensitivity testing revealed a strain of N. nova resistant to trimethoprim-sulfamethoxazole. The antibiotics were thereupon switched to linezolid and meropenem. Unfortunately, the patient died due to a refractory septic shock with multi-organ failure. Infections due to the Nocardia genus are rare and usually occur in patients with underlying immunodeficiencies. Pulmonary disease is the most frequent presentation and pleural effusion is common. Disseminated disease with central nervous system and skin involvement is also frequent. A correct microbiological diagnosis, species identification and sensitivity testing are of utmost importance because of the high intra- and interspecies differences. The strain isolated in this case had an unexpected resistance to trimethoprim-sulfamethoxazole, which is considered to be the cornerstone treatment of a Nocardia infection.

Microbiological hazard identification in river waters used for recreational activities

Pathogenic bacteria, viruses, and parasites can cause waterborne disease outbreaks. The study of coastal water quality contributes to identifying potential risks to human health and to improving water management practices. The Río de la Plata River, a wide estuary in South America, is used for recreational activities, as a water source for consumption and as a site for sewage discharges. In the present study, as the first step of a quantitative microbial risk assessment of the coastal water quality of this river, a descriptive study was performed to identify the microbial pathogens prevalent in its waters and in the sewage discharged into the river. Two sites, representing two different potential risk scenarios, were chosen: a heavily polluted beach and an apparently safe beach. Conductivity and fecal contamination indicators including enterococci, Escherichia coli, F + RNA bacteriophages, and human polyomaviruses showed high levels. Regarding enterococci, differences between sites were significant (p-values <0.001). 93.3% and 56.5% of the apparently safe beach exceeded the recreational water limits for E. coli and enterococci. Regarding pathogens, diarrheagenic E. coli, Salmonella, and noroviruses were detected with different frequencies between sites. The parasites Cryptosporidium spp. and Giardia duodenalis were frequently detected in both sites. The results regarding viral, bacterial, and parasitic pathogens, even without correlation with conventional indicators, showed the importance of monitoring a variety of microorganisms to determine water quality more reliably and accurately, and to facilitate further studies of health risk assessment. The taxonomic description of microbial pathogens in river waters allow identifying the microorganisms that infect the population living on its shores but also pathogens not previously reported by the clinical surveillance system.

Accuracy of an AI-based automated plate reading mobile application for the identification of clinical mastitis-causing pathogens in chromogenic culture media

Using on-farm microbiological culture (OFC), based on chromogenic culture media, enables the identification of mastitis causing pathogens in about 24 h, allows rapid decision making on selective treatment and control management measures of cows with clinical mastitis (CM). However, accurate interpretation of OFC results requires trained and experienced operators, which could be a limitation for the use of OFC in dairy farms. Our hypothesis was that AI-based automated plate reading mobile application can analyze images of microorganisms’ colonies in chromogenic culture media with similar diagnostic performance as a trained specialist evaluator. Therefore, the aim of the present study was to evaluate the diagnostic accuracy of an AI-based application (Rumi; OnFarm, Piracicaba, São Paulo, Brazil) for interpreting images of mastitis causing microorganism colonies grown in chromogenic culture media. For this study two trials were organized to compare the results obtained using an AI-based application Rumi with the interpretation of: (1) a trained specialist, using MALDI-TOF MS as the gold standard; (2) farm personnel users (FPU). In trial 1, a total of 476 CM milk samples, from 11 farms located in São Paulo (n = 7) and Minas Gerais (n = 4), southeast Brazil, were inoculated in chromogenic culture media plates (Smartcolor 2, OnFarm, Piracicaba, São Paulo, Brazil) by specialists under lab conditions, and digital images were recorded 24 h after incubation at 37 °C. After that, all the 476 digital images were analyzed by the Rumi and by another specialist (who only had access to the digital images) and the diagnostic accuracy indicators sensitivity (Se) and specificity (Sp) were calculated using MALDI-TOF MS microbiological identification of the isolates as the reference. In Trial 2, a total of 208 CM milk samples, from 150 farms from Brazil, were inoculated in chromogenic culture media plates by FPU, and the results of microbiological growth were visually interpreted by FPU under on-farm conditions. After visual interpretation, results were recorded using an OnFarmApp application (herd manage application for mastitis by OnFarm, Piracicaba, São Paulo, Brazil), and the images of the chromogenic culture plates were captured by the OnFarmApp to be evaluated by Rumi and Bayesian Latent Class Models were performed to compare Rumi and the FPU. In Trial 1, Rumi presented high and intermediate accuracy results, with the only exception of the low Enterococcus spp.’s Se. In comparison with the specialist, Rumi performed similarly in Se and Sp for most groups of pathogens, with the only exception of non-aureus staphylococci where Se results were lower. Both Rumi and the specialist achieved Sp results > 0.96. In Trial 2, Rumi had similar results as the FPU in the Bayesian Latent Class Model analysis. In conclusion, the use of the AI-based automated plate reading mobile application can be an alternative for visual interpretation of OFC results, simplifying the procedures for selective treatment decisions for CM based on OFC.

Pediatric intracranial empyema complicating otogenic and sinogenic infection

ObjectiveTo describe and compare clinical and microbiological features, surgical and medical management, and outcomes of children with otogenic and sinogenic intracranial empyema (IE) in an institution with an established multidisciplinary protocol. To use the study findings to inform and update the institutional algorithm. MethodsRetrospective analysis was carried out on the electronic healthcare records of all children with oto-sinogenic IE admitted in a 5-year period. ResultsA total of 76 patients were identified and treated according to an institutional protocol. Two distinct groups were identified: intracranial empyema related to otogenic infection (OI-IE, n = 36) or sinogenic infection (SI-IE, n = 40). SI-IE was seen in older children and had a significantly higher morbidity. Sub-dural IE was seen in a minority (n = 16) and only in SI-IE and required urgent collaborative ENT-neurosurgery. Extra-dural IE occurred more frequently and was seen in both SI-IE and OI-IE. No death and overall low morbidity were observed. Particularities found in SI-IE and OI-IE groups (as thrombosis, microbiology, antibiotic treatment, duration and outcome) permitted the delineation of these groups in our updated algorithm. ConclusionThe presence of a collaborative multidisciplinary protocol permits the step-wise co-ordination of care for these complex patients in our institution. All patients received prompt imaging, urgent surgical intervention, and antibiotic treatment. Microbiological identification was possible for each patient and antibiotic rationalization was permitted through use of Polymerase chain reaction (PCR) testing in cases of sterile cultures. Of note, intracranial empyema related to sinogenic infection is shown to have significantly more severe clinical presentation, a higher morbidity, and a longer duration of antibiotic therapy than that related to otogenic infection. Study findings allowed for the update and clarification of the institutional protocol, which now clearly demarcates the clinical presentation, biological evidence, radiology, surgical and medical treatments in children with oto-sinogenic IE.

Screening of Azo-Dye-Degrading Bacteria from Textile Industry Wastewater-Activated Sludge

This study investigates the biodegradation of Reactive Red 141 (RR 141), an azo dye prevalent in the textile industry, by bacteria isolated from activated sludge in a textile effluent treatment plant. RR 141, characterized by nitrogen–nitrogen double bonds (-N=N-), contributes to environmental issues when improperly disposed of in textile effluents, leading to reduced oxygen levels in water bodies, diminished sunlight penetration, and the formation of potentially carcinogenic and mutagenic aromatic amines. This research focuses on identifying bacteria from activated sludge with the potential to decolorize RR 141. Microbiological identification employs MALDI-TOF-MS, known for its precision and rapid identification of environmental bacteria, enhancing treatment efficiency. Results highlight Bacillus thuringiensis and Kosakonia radicincitans as the most promising strains for RR 141 decolorization. Analysis of micro-organisms in activated sludge and database exploration suggests a correlation between these strains and the decolorization process. It is worth noting that this is the first report on the potential use of K. radicincitans for azo dye decolorization. Three distinct culture media—BHI, MSG, and MS—were assessed to investigate their impact on RR 141 decolorization. Notably, BHI and MSG media, incorporating a carbon source, facilitated the bacterial growth of both tested species (B. thuringiensis and K. radicincitans), a phenomenon absent in the MS medium. This observation suggests that the bacteria exhibit limited capability to utilize RR 141 dye as a carbon source, pointing towards the influence of the culture medium on the discoloration process. The study evaluates performance kinetics, decolorization capacity through UV-VIS spectrophotometry, potential degradation pathways via HPLC-MS analysis, phytotoxicity, and enzymatic activity identification. B. thuringiensis and K. radicincitans exhibit potential in decolorizing RR141, with 38% and 26% removal individually in 120 h. As a consortium, they achieved 36% removal in 12 h, primarily through biosorption rather than biodegradation, as indicated by HPLC-MS analyses. In conclusion, the research emphasizes the importance of exploring bacteria from activated sludge to optimize azo dye degradation in textile effluents. B. thuringiensis and K. radicincitans emerge as promising candidates for bioremediation, and the application of MALDI-TOF-MS proves invaluable for rapid and precise bacteria identification.

A web-based microbiological hazard identification tool for infant foods

An integrated approach to identify and assess Microbiological Hazards (MHs) and mitigate risks in infant food chains is crucial to ensure safe foods for infants and young children.A systematic procedure was developed to identify MHs in specific infant foods. This includes five major steps: 1) relevant hazard-food pairing, 2) process inactivation efficiency, 3) recontamination possibility after processing, 4) MHs growth opportunity, and 5) MHs-food association level. These steps were integrated into an online tool called the Microbiological Hazards IDentification (MiID) decision support system (DSS), targeting food companies, governmental agencies and academia users, and is accessible at https://foodmicrobiologywur.shinyapps.io/Microbial_hazards_ID/. The MiID DSS was validated in four case studies, focussing on infant formula, fruit puree, cereal-based meals, and fresh fruits, each representing distinct products and processing characteristics. The results obtained through the application of the MiID DSS, compared with identification by food safety experts, consistently identified the top MHs in these food products. This process affirms its effectiveness in systematic hazard identification.The introduction of the MiID DSS helps to structure the first steps in HACCP (hazard analysis) and in risk assessment (hazard identification) to follow a structured and well-documented procedure, balancing the risk of overlooking relevant MHs or including too many irrelevant MHs. It is a valuable addition to risk analysis/assessment in infant food chains and has the potential for future extension. This includes the incorporation of newly acquired data related to infant foods via a semi-publicly hosted platform, or it can be adapted for hazard identification in general food products using a similar framework.

Frequency Survey of Bacterial Contamination of Mobile Cell Phones in General Population in Tehran, Iran

Background: Mobile smart phones have become increasingly integrated into the daily lives of individuals in society. Recent studies indicated the considerable role of these devices as reservoirs for various micro-organisms. The objective of this study was to assess the prev­alence of microbiological contamination of mobile phones in general population. Materials and Methods: This cross-sectional study included a large sample of mobile phones of gen­eral population Tehran in 2015. Samples for culture were collected from mobile phones and transported for microbiological identification based on standard laboratory methods. Results: Bacteriological analysis revealed that in total of 5220 sample retrieved, 5180 (98.9%) mobile phone devices were contaminated with bacteria. The most common microorganisms that were isolated include: Staphylococcus epidermidis (63.9), Escherichia coli (12.3%) and Staphylo­coccus aureus (11.4%). Conclusion: The prevalence of mobile phone contamination is high in general population in Tehran. Although most of the isolated organisms seemed to be non-patho­genic, their colonization may endanger certain populations particularly in health care settings. [GMJ.2016;5(2):70-74]

Low Occurrence of Salmonella spp. in Wild Animals in Bahia, Brazil-Population Assessment and Characterization in the Caatinga and Atlantic Forest Biomes.

Salmonella spp. are known to persist in the environment. Wild animals are believed to act as important reservoirs, with antimicrobial resistance frequently occurring in the environment. However, little is known about the role of the wildlife in Bahia as a reservoir for Salmonella in Brazil. This study aimed to isolate and characterize Salmonella spp. from wildlife in the Atlantic Forest and Caatinga biomes considering indicators such as the animal species, degree of anthropization, sampling area, and feeding habits. Convenience wildlife sampling and characterization were conducted, followed by microbiological and molecular identification of Salmonella isolates, serotyping, and antimicrobial susceptibility testing. A total of 674 fecal samples were collected from 12 municipalities during 2015-2021, and 4 were positive for the following Salmonella species: Salmonella enterica subspecies enterica serovar Agona (n = 1), Salmonella enterica subsp. enterica serogroup O:16 (n = 2), and Salmonella enterica subsp. enterica serovar Muenchen (n = 1). Antimicrobial susceptibility analysis revealed that one isolate was resistant to six antibiotics, including extended-spectrum penicillins and beta-lactamase inhibitors. These results indicated a low frequency of Salmonella spp. in the sampled forest fragments. The presence of Salmonella in wild animals increases the risk to public health and biodiversity and indicates that they can act as sentinels of environmental contamination or indicators of preservation.